Genome-Wide Analysis of Nitrate Transporter (NRT/NPF) Family in Sugarcane Saccharum spontaneum L.

Nitrate is the predominant nitrogen source for plant growth and development. However, sugarcane, globally used as the primary sugar crop and biofuel feedstock, displays a low nitrate use efficiency due to a low capacity in storing nitrate in shoots. It is well studied that the nitrate transporter (NRT/NPF) family functions as the gatekeeper in governing nitrogen uptake and distribution, and optimizing nitrogen utilization in plants. This makes it a promising target for improving nitrogen use efficiency in sugarcane. Here, we carried out a comprehensive analysis of NRT/NPF genes at a genome-wide scale in Saccharum spontaneum. A BLAST search of NRT/NPF genes was initially performed against recently released sugarcane genome, followed by phylogenetic, gene structure and protein motif analysis. Additionally, NRT/NPF gene expression profile from various tissues was obtained from RNA-seq data analysis. As a result, we identified 178 NPF, 20 NRT2, and 6 NRT3 genes which spread across all 8 monoploid chromosomes. NPF and NRT3 exhibit high levels of genetic diversities as opposed to NRT2 which is more evolutionarily conserved. Interestingly, several SsNPF genes are products of gene fusions of several tandem duplications, which provide valuable structural resources for functional characterization of nitrate transporters. Moreover, several genes are tissue-specific expressed, indicating roles in tissue-specific nitrate translocations. A substantial number of NRT/NPF genes are heterogeneous in terms of their gene structures and mRNA abundance. Taken together, our work provides a genetic foundation for future investigations of molecular and physiological functions of sugarcane nitrate transporters.